Jim Procter [Wed, 13 Jul 2016 15:52:20 +0000 (16:52 +0100)]
Merge branch 'features/JAL-2110_crossRefDuplications' into develop
Jim Procter [Wed, 13 Jul 2016 15:51:30 +0000 (16:51 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
tcofoegbu [Wed, 13 Jul 2016 10:28:11 +0000 (11:28 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 13 Jul 2016 10:28:06 +0000 (11:28 +0100)]
JAL-2135 minor house-keeping
Jim Procter [Tue, 12 Jul 2016 16:41:50 +0000 (17:41 +0100)]
JAL-2144 TODO - new methods for canonicalisation and comparison of source strings, regularisation of properties from SequenceDbSource implementations, recognition of coding databases in a more generic way.
Jim Procter [Tue, 12 Jul 2016 16:28:55 +0000 (17:28 +0100)]
JAL-2110 avoid potential race condition where user changes selection after ‘show cross refs’ option has been selected
Jim Procter [Tue, 12 Jul 2016 16:19:43 +0000 (17:19 +0100)]
JAL-2110 TODO for JAL-2131
Jim Procter [Tue, 12 Jul 2016 16:18:06 +0000 (17:18 +0100)]
JAL-2110 note about use case for when alignAsSameSequences fails due to missing shared dataset refs
Jim Procter [Tue, 12 Jul 2016 16:15:23 +0000 (17:15 +0100)]
JAL-2110 test demonstrating limitation of current implementation of alignAs (simple case)
Jim Procter [Tue, 12 Jul 2016 16:14:28 +0000 (17:14 +0100)]
JAL-2110 javadoc and TODO re shortcomings of implementation
Jim Procter [Tue, 12 Jul 2016 16:12:10 +0000 (17:12 +0100)]
JAL-2110 javadoc
Jim Procter [Tue, 12 Jul 2016 15:37:19 +0000 (16:37 +0100)]
JAL-2110 scalability todo
Jim Procter [Tue, 12 Jul 2016 15:36:31 +0000 (16:36 +0100)]
JAL-1381 JAL-2110 efficiency TODO
Jim Procter [Tue, 12 Jul 2016 10:35:18 +0000 (11:35 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 12 Jul 2016 10:31:52 +0000 (11:31 +0100)]
JAL-1369 release notes for patch of save/restore representative group when only one sequence represented
tcofoegbu [Tue, 12 Jul 2016 10:03:50 +0000 (11:03 +0100)]
JAL-2135 NPE bugfix when parsing a structure file with Jmol and id & inFile is null
gmungoc [Sat, 9 Jul 2016 06:12:09 +0000 (07:12 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
tcofoegbu [Fri, 8 Jul 2016 16:16:54 +0000 (17:16 +0100)]
JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be configurable. Minor refactorings (StructureViewSettings class renamed to StructureImportSettings, fileName variables of AlignFile class renamed to dataObject since in realty it could be a file, url or pasted string)
gmungoc [Thu, 7 Jul 2016 15:51:51 +0000 (16:51 +0100)]
JAL-2110 added alignAsSameSequences to handle 'direct' (copy) case
gmungoc [Thu, 7 Jul 2016 15:51:21 +0000 (16:51 +0100)]
JAL-2110 field 'cf' moved to stack
gmungoc [Wed, 6 Jul 2016 15:34:32 +0000 (16:34 +0100)]
JAL-2110 generic rather than specific check for gap character
gmungoc [Wed, 6 Jul 2016 15:34:01 +0000 (16:34 +0100)]
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented
gmungoc [Wed, 6 Jul 2016 12:08:28 +0000 (13:08 +0100)]
JAL-2110 ensuring mapped dbrefs between protein and cds
gmungoc [Wed, 6 Jul 2016 11:47:04 +0000 (12:47 +0100)]
JAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL CDS protein_id)
gmungoc [Wed, 6 Jul 2016 11:42:11 +0000 (12:42 +0100)]
JAL-2110 cross-refs from protein to show cds not non-coding sequences
gmungoc [Wed, 6 Jul 2016 09:10:53 +0000 (10:10 +0100)]
JAL-2110 fixes and tests for adding dbrefs to EMBL sequence and products
gmungoc [Mon, 4 Jul 2016 14:57:01 +0000 (15:57 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Mon, 4 Jul 2016 14:35:13 +0000 (15:35 +0100)]
JAL-2110 use shared dataset when copying alignment for split frame
gmungoc [Mon, 4 Jul 2016 14:34:51 +0000 (15:34 +0100)]
JAL-2110 added another test case (should fail but doesn't)
gmungoc [Mon, 4 Jul 2016 14:27:21 +0000 (15:27 +0100)]
Revert "JAL-2110 use shared alignment dataset when copying alignment for split frame"
This reverts commit
f931c557266d95b3f4ab5b64bd108123c90e85ab.
gmungoc [Mon, 4 Jul 2016 14:21:49 +0000 (15:21 +0100)]
JAL-2110 use shared alignment dataset when copying alignment for split
frame
gmungoc [Mon, 4 Jul 2016 14:21:17 +0000 (15:21 +0100)]
JAL-2110 bug fix / test for searchDataset mappings created
gmungoc [Mon, 4 Jul 2016 14:20:27 +0000 (15:20 +0100)]
JAL-2110 unused method removed
gmungoc [Mon, 4 Jul 2016 14:19:43 +0000 (15:19 +0100)]
JAL-2110 defensive check in code
gmungoc [Fri, 1 Jul 2016 15:54:01 +0000 (16:54 +0100)]
JAL-2110 bug fixing and tidying for get cross-refs
gmungoc [Fri, 1 Jul 2016 14:01:00 +0000 (15:01 +0100)]
JAL-2110 set reasonable bounds to initial split of SplitFrame divider
tcofoegbu [Fri, 1 Jul 2016 10:08:43 +0000 (11:08 +0100)]
JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2
gmungoc [Fri, 1 Jul 2016 09:19:20 +0000 (10:19 +0100)]
JAL-2110 add 'products' parameter to filter results in madeCdsAlignment
gmungoc [Fri, 1 Jul 2016 09:07:31 +0000 (10:07 +0100)]
JAL-2110 code/comment tidy
gmungoc [Thu, 30 Jun 2016 15:24:19 +0000 (16:24 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
tcofoegbu [Thu, 30 Jun 2016 14:59:00 +0000 (15:59 +0100)]
JAL-2074 Improvement to StructureChooser and FTS interfaces to remember the user preferences for summary table columns, window size & positions
gmungoc [Thu, 30 Jun 2016 14:49:51 +0000 (15:49 +0100)]
JAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN dbrefs
gmungoc [Thu, 30 Jun 2016 13:01:23 +0000 (14:01 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
tcofoegbu [Thu, 30 Jun 2016 09:46:51 +0000 (10:46 +0100)]
JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable proper processing of mmCIF files
tcofoegbu [Wed, 29 Jun 2016 13:58:41 +0000 (14:58 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 29 Jun 2016 13:58:34 +0000 (14:58 +0100)]
JAL-1479 added test case to elaborate getEntityByMostOptimalMatchedId method
gmungoc [Wed, 29 Jun 2016 13:21:32 +0000 (14:21 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Wed, 29 Jun 2016 12:48:58 +0000 (13:48 +0100)]
JAL-1270 avoid overwriting .jalview_properties with test service urls
tcofoegbu [Wed, 29 Jun 2016 11:34:51 +0000 (12:34 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 29 Jun 2016 11:34:41 +0000 (12:34 +0100)]
JAL-1479 improved Sifts PID calculation for determining an Entity to process
gmungoc [Wed, 29 Jun 2016 10:36:16 +0000 (11:36 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
gmungoc [Wed, 29 Jun 2016 08:17:29 +0000 (09:17 +0100)]
JAL-1369 fix bug reloading a project with group sequence reps
tcofoegbu [Tue, 28 Jun 2016 15:21:17 +0000 (16:21 +0100)]
JAL-1479 minor refactor and housekeeping
tcofoegbu [Tue, 28 Jun 2016 14:28:28 +0000 (15:28 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 28 Jun 2016 14:28:22 +0000 (15:28 +0100)]
JAL-1479 improved SiftsClient test coverage and implemented previously unimplemented test cases
gmungoc [Mon, 27 Jun 2016 13:04:14 +0000 (14:04 +0100)]
tidied loop with generic iteration / loop variable
gmungoc [Mon, 27 Jun 2016 13:03:09 +0000 (14:03 +0100)]
JAL-2133 refactored duplicated code to AlignmentViewport
gmungoc [Mon, 27 Jun 2016 13:02:15 +0000 (14:02 +0100)]
JAL-1369 additional asserts in testStoreAndRecoverReferenceSeqSettings
gmungoc [Mon, 27 Jun 2016 12:35:51 +0000 (13:35 +0100)]
JAL-1270 unit tests for HiddenSequences
tcofoegbu [Fri, 24 Jun 2016 10:09:15 +0000 (11:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 24 Jun 2016 10:08:59 +0000 (11:08 +0100)]
JAL-1960 updated unit test to include the test case where a sequences has no PDBId entry(s) but has Uniprot & PDB dbrefs
gmungoc [Thu, 23 Jun 2016 14:26:03 +0000 (15:26 +0100)]
JAL-2130 now simply viewer.dispose() to close down Jmol threads
Jim Procter [Thu, 23 Jun 2016 13:58:42 +0000 (14:58 +0100)]
Merge branch 'develop' into merge_JAL-2110
tcofoegbu [Thu, 23 Jun 2016 13:47:20 +0000 (14:47 +0100)]
JAL-1996 added notes for an alternative way to view example pages source code
Jim Procter [Thu, 23 Jun 2016 13:16:55 +0000 (14:16 +0100)]
JAL-1270 test group fix
Jim Procter [Thu, 23 Jun 2016 13:15:05 +0000 (14:15 +0100)]
JAL-2110 make indirect xref searches work by not filtering refs on candidates after selecting them by molecule type (direct==same, indirect==different)
Jim Procter [Thu, 23 Jun 2016 13:12:09 +0000 (14:12 +0100)]
JAL-2110 warning message when routine finds non-ds sequences in the dataset (seems to happen with alignments returned from Ensembl sequence fetcher)
Jim Procter [Thu, 23 Jun 2016 13:11:27 +0000 (14:11 +0100)]
JAL-2110 clarify javadoc
Jim Procter [Thu, 23 Jun 2016 13:11:10 +0000 (14:11 +0100)]
JAL-2110 refactor to split SequenceFetcher from x-ref resolution routine
Jim Procter [Thu, 23 Jun 2016 13:09:44 +0000 (14:09 +0100)]
JAL-2110 JAL-1551 formatting
Jim Procter [Thu, 23 Jun 2016 13:09:36 +0000 (14:09 +0100)]
JAL-2110 enable and fix failing tests
Jim Procter [Thu, 23 Jun 2016 13:06:10 +0000 (14:06 +0100)]
JAL-2110 enable and fix test
Jim Procter [Thu, 23 Jun 2016 13:04:47 +0000 (14:04 +0100)]
JAL-2110 refactor sequenceFetcherTest to allow verifying cross-reference retrieval for a single sequence sourc
Jim Procter [Thu, 23 Jun 2016 13:02:38 +0000 (14:02 +0100)]
JAL-2110 use SequenceI.isProtein()
Jim Procter [Thu, 23 Jun 2016 13:01:36 +0000 (14:01 +0100)]
JAL-2110 SequenceI.isProtein method
tcofoegbu [Wed, 22 Jun 2016 16:03:00 +0000 (17:03 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 22 Jun 2016 16:02:53 +0000 (17:02 +0100)]
JAL-1996 added link for viewing example source codes, changed release history outline from list to table
gmungoc [Wed, 22 Jun 2016 15:09:00 +0000 (16:09 +0100)]
JAL-2015 fixed bug in copy constructor and added tests
gmungoc [Wed, 22 Jun 2016 13:56:32 +0000 (14:56 +0100)]
JAL-1982 defensive checks for null annotations array
gmungoc [Wed, 22 Jun 2016 13:00:08 +0000 (14:00 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 22 Jun 2016 12:59:35 +0000 (13:59 +0100)]
JAL-1982 defensive test for null array of annotations
tcofoegbu [Wed, 22 Jun 2016 11:54:43 +0000 (12:54 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 22 Jun 2016 11:54:34 +0000 (12:54 +0100)]
JAL-1996 removed quick links in example pages, added one minimal applet embedding example to applet deployment page
Jim Procter [Wed, 22 Jun 2016 10:41:24 +0000 (11:41 +0100)]
JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide()’ flag
Jim Procter [Tue, 21 Jun 2016 15:13:05 +0000 (16:13 +0100)]
Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110
Jim Procter [Tue, 21 Jun 2016 14:58:43 +0000 (15:58 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
gmungoc [Tue, 21 Jun 2016 14:27:33 +0000 (15:27 +0100)]
JAL-2074 suppress prompt to save closed Groovy script on Jalview Quit
gmungoc [Tue, 21 Jun 2016 14:26:16 +0000 (15:26 +0100)]
JAL-1270 remove test artefact file after test
Jim Procter [Tue, 21 Jun 2016 13:53:15 +0000 (14:53 +0100)]
Merge branch 'features/JAL-1956_featureStyles' into merge_JAL-1956
Jim Procter [Tue, 21 Jun 2016 13:45:56 +0000 (14:45 +0100)]
JAL-1270 ensure before/after clauses have at least alwaysRun=true in them
gmungoc [Tue, 21 Jun 2016 13:41:43 +0000 (14:41 +0100)]
JAL-1270 added runAlways=true to setUp method
gmungoc [Tue, 21 Jun 2016 13:41:08 +0000 (14:41 +0100)]
JAL-2074 reuse Groovy window when reopening; rebind Cmd-Q to Jalview
when closing
Jim Procter [Tue, 21 Jun 2016 09:54:17 +0000 (10:54 +0100)]
JAL-2089 cleared out old ‘What’s new’
Jim Procter [Tue, 21 Jun 2016 09:53:31 +0000 (10:53 +0100)]
JAL-192 JAL-1369 release notes
Jim Procter [Tue, 21 Jun 2016 09:45:56 +0000 (10:45 +0100)]
Merge branch 'features/JAL-1369_refseqproject' into develop
Jim Procter [Tue, 21 Jun 2016 09:40:47 +0000 (10:40 +0100)]
JAL-1369 make sure desktop is cleared before test starts
Jim Procter [Tue, 21 Jun 2016 09:40:19 +0000 (10:40 +0100)]
JAL-1369 jalview2xml tests need to be run sequentially
gmungoc [Tue, 21 Jun 2016 09:38:48 +0000 (10:38 +0100)]
JAL-2110 updated unit test to match code changes
Jim Procter [Tue, 21 Jun 2016 09:22:57 +0000 (10:22 +0100)]
JAL-1369 mark reference sequence & view state and restore it
Jim Procter [Tue, 21 Jun 2016 09:22:02 +0000 (10:22 +0100)]
JAL-1369 project XML efficiency TODO
git://source.jalview.org / jalview.git / log